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comparison rename_annotated_feature.xml @ 0:268fcec93d9c draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
author recetox
date Tue, 21 May 2024 07:44:25 +0000
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-1:000000000000 0:268fcec93d9c
1 <tool id="rename_annotated_feature" name="Rename Annotated Feature" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>Rename columns in abundance table based on annotations table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creator"/>
7 <requirements>
8 <requirement type="package" version="2.2.1">pandas</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 python3 '${__tool_directory__}/rename_annotated_feature.py'
12 --annotations_table_path '$annotations_table_path'
13 --abundance_table_path '$abundance_table_path'
14 --mode '$mode'
15 --output_path '$output_path'
16 ]]></command>
17 <inputs>
18 <param name="annotations_table_path" type="data" format="tabular" label="Annotations table file" help="Path to the annotations table file."/>
19 <param name="abundance_table_path" type="data" format="tabular" label="Abundance table file" help="Path to the abundance table file."/>
20 <param name="mode" type="select" label="Mode to use for renaming" help="Can be single or multiple.">
21 <option value="single" selected="true">Single</option>
22 <option value="multiple">Multiple</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data name="output_path" format="tabular" label="Renamed abundance table"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/>
31 <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular"/>
32 <param name="mode" value="single"/>
33 <output name="output_path" file="single_mode_output.tsv"/>
34 </test>
35 <test>
36 <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/>
37 <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular" />
38 <param name="mode" value="multiple"/>
39 <output name="output_path" file="multi_mode_output.tsv"/>
40 </test>
41 </tests>
42 <help>
43 <![CDATA[
44 @HELP@
45 ]]>
46 </help>
47 <!-- Update to the correct citation for this tool -->
48 <citations>
49 <citation type="doi">10.5281/zenodo.7178586</citation>
50 <citation type="doi">10.21105/joss.02411</citation>
51 <citation type="doi">10.1021/ac501530d</citation>
52 </citations>
53 </tool>